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- EMDB-5183: The structure of JC polyomavirus (pH 7.4) -

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Basic information

Entry
Database: EMDB / ID: 5183
TitleThe structure of JC polyomavirus (pH 7.4)
KeywordsJC / JCV / polyomavirus
SampleJC polyomavirus in buffer A (pH 7.4)
SourceJC polyomavirus / virus / JCV
Map dataCryo-EM reconstruction of JC polyomavirus (pH 7.4)
Methodsingle particle (icosahedral) reconstruction, at 19 A resolution
AuthorsShen PS / Enderlein D / Nelson C / Carter WS / Kawano M / Xing L / Swenson RD / Olson NH / Baker TS / Cheng RH / Atwood WJ / Johne R / Belnap DM
CitationVirology, 2011, 411, 142-152

Virology, 2011, 411, 142-152 StrPapers
The structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4.
Peter S Shen / Dirk Enderlein / Christian D S Nelson / Weston S Carter / Masaaki Kawano / Li Xing / Robert D Swenson / Norman H Olson / Timothy S Baker / R Holland Cheng / Walter J Atwood / Reimar Johne / David M Belnap

DateDeposition: Apr 12, 2010 / Header (metadata) release: Dec 8, 2010 / Map release: Jan 19, 2011 / Last update: Apr 12, 2010

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 43
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 43
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_5183.map.gz (map file in CCP4 format, 193091 KB)
Projections & slices
Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
367 pix
1.62 A/pix
= 597.78 A
367 pix
1.62 A/pix
= 597.78 A
367 pix
1.62 A/pix
= 597.78 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.62 A
Density
Contour Level:43 (by author), 43 (movie #1):
Minimum - Maximum-72.7188 - 139.522
Average (Standard dev.)10.425 (32.6366)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions367367367
Origin-183-183-183
Limit183183183
Spacing367367367
CellA=B=C: 597.78 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.621.621.62
M x/y/z369369369
origin x/y/z0.0000.0000.000
length x/y/z597.780597.780597.780
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-183-183-183
NC/NR/NS367367367
D min/max/mean-72.719139.52210.425

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Supplemental data

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Sample components

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Entire JC polyomavirus in buffer A (pH 7.4)

EntireName: JC polyomavirus in buffer A (pH 7.4) / Number of components: 1 / Oligomeric State: virions

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Component #1: virus, JC polyomavirus

VirusName: JC polyomavirus / a.k.a: JCV / Class: VIRION / Details: Cryo-EM of JC polyomavirus over holey carbon grids / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: JC polyomavirus / virus / JCV
Source (natural)Host Species: Homo sapiens / human / Host category: VERTEBRATES
Shell #1Name of element: VP1 / Diameter: 5000 A / T number(triangulation number): 7

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1.5 mg/ml / Buffer solution: 10 mM Tris, 50 mM NaCl, 0.01 mM CaCl2 / pH: 7.4
Support film200 mesh copper grid (holey carbon)
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 89 K / Humidity: 100 % / Method: 3 second blot before plunging
Details: Vitrification instrument: Vitrobot. vitrification carried out in nitrogen atmosphere

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F30 / Date: Apr 23, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
LensMagnification: 39000 X (nominal), 39000 X (calibrated)
Astigmatism: astigmatism was corrected at 59,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 500 - 4900 nm
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN / Temperature: 90 K ( 88 - 95 K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 50 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns / Bit depth: 16 / Details: Micrographs digitized in positive contrast mode.

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: common lines / Software: PFT2 and EM3DR2 / CTF correction: each micrograph / Resolution: 19 A / Resolution method: FSC 0.333

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